Critical thinking is essential for the children and could help them avoid extremism, say observers.
Education for girls in the Tirah Valley of Khyber District, once a distant dream, is now in full bloom amid the defeat of militants.
The initiative aims to help high school students learn critical thinking skills to reduce the effectiveness of extremist recruiters.
Youth who can't afford a higher education often are the targets of extremist recruiters, analysts say.
Improved security and stability in Khyber Pakhtunkhwa are opening the doors to a modern curriculum for all schoolchildren.
'This is a revolutionary step in a district affected by war,' an education leader said.
Six years after the Taliban forced the school to shutdown, a now safe environment in the city is allowing parents to send their children back.
The reforms aim to limit hate speech in madrassas and create new opportunities for students.
The facility opened in an area that was once the second headquarters of the Tehreek-e-Taliban Pakistan from which it planned and launched attacks.
The country is planning to mainstream more than 30,000 madrassas, putting their management under the Education Ministry, officials say.